6DZS

Mycobacterial homoserine dehydrogenase ThrA in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb6DZS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium hassiacum DSM 44199
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-05 Released: 2018-07-18 
• Deposition Author(s): Chaton, C.T., Rodriguez, E.S., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.245 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Structure of mycobacterial homoserine dehydrogenase ThrA

Chaton, C.T., Rodriguez, E.S., Korotkov, K.V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 185.04 kDa 
• Atom Count: 12,655 
• Modelled Residue Count: 1,712 
• Deposited Residue Count: 1,764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A, B, C, D	441	Mycolicibacterium hassiacum DSM 44199	Mutation(s): 0  Gene Names: hom, C731_3131 EC: 1.1.1.3
UniProt
Find proteins for K5BJC9 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)) Explore K5BJC9  Go to UniProtKB:  K5BJC9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.245 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.8	α = 90
b = 110.32	β = 91.83
c = 97.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Chaton, C.T., Rodriguez, E.S., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103486
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description